Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 116

System / cell line: cohort ✕ Assay: scrna ✕ Clear

Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

crc epcam+ aggregated cancer scrna-seq copy pseudobulk
Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn
Divergent macrophage-regulated T cell states determine response to Bacillus Calmette-Guérin vaccine in high-risk bladder cancer.

PMID 42081487 · PMC13262731 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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BCG responders show an increase in Th17-like Th1 CD4+ T cells with greater proinflammatory cytokine expression

bladder pbmcs cd4+ separate scrna-seq trajectory flow
Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide
Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 63

Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune
Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

PMID 41229397 · PMC12604667 · NAR genomics and bioinformatics · 2025 · 8 claims · 4 setups

Has reproduction · 75

scIGD is a Snakemake workflow that automates HLA allele-typing and allele-specific expression quantification from scRNA-seq data

aida merkel-cell 20k myeloma scrna-seq
Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

PMID 41706364 · PMC12916967 · Cellular oncology (Dordrecht, Netherlands) · 2026 · 7 claims · 8 setups

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Cholesterol metabolic activity is markedly elevated in HCC tumors and in immune checkpoint blockade (ICB) non-responders, with pronounced intratumoral heterogeneity across malignant cell subpopulations

hcc tcga-lihc malignant hepa1-6 scrna-seq bulk hdwgcna
Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

PMID 41807578 · PMC13230996 · Molecular systems biology · 2026 · 7 claims · 8 setups

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CSI-TME is a computational pipeline that deconvolves bulk tumor RNA-seq into cell-type-specific expression (via CODEFACS), infers transcriptional states per cell type via ICA, and identifies IC pairs from two cell types whose joint activity is associated with survival via Cox regression

idh-mutant tcga cgga deconvolved scrna-seq bulk independent
Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

PMID 41821037 · PMC12983708 · Genome biology · 2026 · 8 claims · 8 setups

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Horizontal integration of scRNA-seq and snRNA-seq improves cell-type identification

renal kidney pbmc heart scrna-seq snrna-seq snatac-seq
Exploring phenotype-related single-cells through attention-enhanced representation learning.

PMID 41566378 · PMC12906058 · Genome medicine · 2026 · 6 claims · 5 setups

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scPhase, an attention-based multiple instance learning (AMIL) framework with Mixture-of-Experts aggregation, predicts sample-level clinical phenotypes from raw scRNA-seq data and generalizes across patient cohorts

pbmcs brain tumor scrna-seq
scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.

PMID 42013315 · PMC13133615 · Cancer discovery · 2026 · 8 claims · 7 setups

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scSurvival, an attention-based multiple-instance Cox regression framework, models each tumor sample as an ensemble of cells to predict survival outcomes at both patient and single-cell levels

simulated melanoma liver higher scrna-seq differential
A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

crc epithelial rcrc tcga-read scrna-seq copy gene
The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

PMID 42011021 · PMC13096693 · Clinical and translational medicine · 2026 · 6 claims · 8 setups

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KRAS-mutant LUAD patients show significantly poorer pathological response and inferior long-term survival after neoadjuvant immunotherapy compared to KRAS-wildtype patients

resected resectable epithelial cd4t_treg_tnfrsf4 scrna-seq retrospective cnv
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

cervical tcga siha scrna-seq bulk rt-qpcr
Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

PMID 38433919 · PMC10905000 · iScience · 2024 · 8 claims · 8 setups

Has reproduction · 100

The four proposed GBM molecular subtypes (Proneural, Neural, Classical, Mesenchymal / NPC-like, OPC-like, AC-like, MES-like) are not mutually exclusive or independent of one another

scrna-seq tcga-gbm gse131928 tumor gene pairwise principal
Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

PMID 37320872 · PMC10277597 · Translational oncology · 2023 · 8 claims · 9 setups

Has reproduction · 50

Seven distinct CAF subsets exist in HNSCC, identified via integration of scRNA-seq, bulk transcriptomic, and spatial transcriptomic data.

hnscc tcga-hnscc caf fibroblast single-cell bulk spatial
A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

PMID 41514053 · PMC12858409 · Nature cancer · 2026 · 8 claims · 6 setups

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Generated a single-cell Immune Atlas of 1,397,272 BM cells from 337 NDMM participants (263 discovery, 74 validation) using scRNA-seq

cd138 bone ndmm single-cell cytogenetic disease
Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

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TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

pbmcs pbmc cd8+ single-cell cell-type expression
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

Has reproduction · 81

scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell
Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.

PMID 41488744 · PMC12764181 · International journal of genomics · 2026 · 8 claims · 8 setups

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Epithelial and endothelial cells show the highest anoikis-enriched scores among LUAD TME cell types, with AT2-like Epi being the most anoikis-related epithelial subpopulation.

luad pan-cancer tumor scrna-seq spatial bulk

Experiments

Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

Divergent macrophage-regulated T cell states determine response to Bacillus Calmette-Guérin vaccine in high-risk bladder cancer.

Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

Allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data.

Single-cell mapping of cholesterol metabolism reveals FDPS as a therapeutic vulnerability in hepatocellular carcinoma.

Identifying clinically relevant cell state interactions in the tumor microenvironment of IDH-mutant gliomas using CSI-TME.

Systematic evaluation of single-cell multimodal data integration enhances cell type resolution and discovery of clinically relevant states in complex tissues.

Exploring phenotype-related single-cells through attention-enhanced representation learning.

scSurvival: Single-Cell Survival Analysis of Clinical Cancer Cohort Data at Cellular Resolution.

A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

The landscape of responses to neoadjuvant immunotherapy in resectable Kirsten rat sarcoma viral oncogene homolog-mutant lung adenocarcinoma: Clinical heterogeneity and correlative immunologic analysis.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

Proneural-mesenchymal antagonism dominates the patterns of phenotypic heterogeneity in glioblastoma.

Heterogeneity of cancer-associated fibroblasts in head and neck squamous cell carcinoma.

A single-cell atlas characterizes dysregulation of the bone marrow immune microenvironment associated with outcomes in multiple myeloma.

Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

Advancing Prognosis Prediction and Immunotherapy Efficacy in Lung Adenocarcinoma Through Machine Learning: Novel Insights From Anoikis Regulator Patterns in Single-Cell Multiomics.